Hello,
I can't seem to get the energetic contribution from distance
restraints in gmx 3.3.1, 3.3.3, or 4.0
I am using Mark Abraham's incantation of the charmm ff in gromacs.
Here, distance_restraints are used to deal with Charmm's Urey-Bradley
potentials. My colleague is using some non-standard charmm parameters,
so I also used the scripts from the gromacs site to convert our
parameter files to gromacs format and included them in ffcharmm. I
believe that I have done everything correctly, but I want to check
that the energy of a given snapshot is the same when calculated by
gromacs as it is in NAMD (which reads the charmm files directly). Most
energies are looking close enough to be rounding errors, but my angle
energy is off. I suspect that the distance restraint energy plus the
angle energy will be the same as the angle energy as stated by NAMD,
but I do need to be sure here. I don't see any indication of the
distance restraint energy in the .log file or by g_energy.
I know others have been using the charmm forcefield, and I am
wondering how they solved this problem. Perhaps I have done something
incorrectly, but if the distance restraint energy is in fact not
accessible, then this is also a suggestion to include that in the .edr
file for gmx 4.1.
Thanks,
Chris.